As long as the top bolt of the stem's steerer clamp is below the top of the steerer, you are fine. My preference is to have the steerer long enough to project slightly above the top of the stem and add a spacer above the stem to give me a 3-4 mm gap below the top of that spacer. That accomplishes the gap needed to adjust the headset and assures the steerer is fully supported by the stem. This is particularly useful with a carbon steerer.